Which version of freesurfer are you running? At one point, reg-feat2anat was dependent on the feat registration, but "now" it is not. I don't know whether you fall into the "now" category. If you have a partial FOV, then it will probably fail. You can test this by running bbregister outside of the reg-feat2anat. You can look in the reg-feat2anat for a command line, but it should be something like:
bbregister --s subject --mov example_func.nii.gz --bold --init-fsl --reg register.dat If this fails, you have a couple of options. If the functional and anatomical were acquired in the same session, then you can use --init-header instead of --init-fsl. If they are not but you have a full-brain of anything acquired during the same session as the functional, you can pass that as an intermediate volume to bbregister (--int). doug Cris Lanting wrote: > Dear all, > > I'm having a slight problem with reg-feat2anat to transform functional > data (FSL) to anatomical (Freesurfer) in that the resulting > transformation seems completely wrong. > What I've done so far is the following: > > 1) run FEAT including the normal FEAT registration (which I know fails > due to a lack of FOV in the functional data) > 2) re-run the Flirt for a proper registration (i.e. by using the > -usesqform option to obtain better registration) > 3) overwrite the example_func2highres.mat, highres2standard.mat and > example_func2standard.mat file with the newly obtained registration > files. > (The resulting files are now properly registered when viewing in e.g. fslview) > 4) Run updatefeatreg <featdir.feat> > 5) Start FEAT and change the mode to run Post-stats only. Select the > FEAT output directory as input. Go into the registration tab and turn > off all registration. Press GO. > (steps 3-5 following the FSL FAQ on custom registration into a FEAT analysis) > > 6) run a complete freesurfer segmentation and all the rest using recon-all etc > 7) reg-feat2anat --feat featdir.feat --subject subjectid > > When I now check the registration, it seems completely wrong... > My guess would be that it has to do with the re-registration in steps > 2-5 but as far as I can tell the files are registered properly to the > anatomy scan (and to the template (or standard), the > MNI152_T1_1mm_brain file) > > Any ideas? > (Not sure whether it is appreciated if I send a screenshot as > attachment, so I'll leave it for now) > > Cheers, > Cris > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
